Accidental ingestion or consumption of supra-therapeutic doses of methadone can result in neurological sequelae in humans. We aimed to determine the neurological deficits of methadone-poisoned patients admitted to a referral poisoning hospital using brain magnetic resonance (MR) and diffusion weighted (DW) imaging. In this retrospective study, brain MRIs of the patients admitted to our referral center due to methadone intoxication were reviewed. Methadone intoxication was confirmed based on history, congruent clinical presentation, and confirmatory urine analysis. Each patient had an MRI with Echo planar T1, T2, FLAIR, and DWI and apparent deficient coefficient (ADC) sequences without contrast media. Abnormalities were recorded and categorized based on their anatomic location and sequence. Ten patients with abnormal MRI findings were identified. Eight had acute- and two had delayed-onset encephalopathy. Imaging findings included bilateral confluent or patchy T2 and FLAIR high signal intensity in cerebral white matter, cerebellar involvement, and bilateral occipito-parietal cortex diffusion restriction in DWI. Internal capsule involvement was identified in two patients while abnormality in globus pallidus and head of caudate nuclei were reported in another. Bilateral cerebral symmetrical confluent white matter signal abnormality with sparing of subcortical U-fibers on T2 and FLAIR sequences were observed in both patients with delayed-onset encephalopathy. Acute- and delayed-onset encephalopathies are two rare adverse events detected in methadone-intoxicated patients. Brain MRI findings can be helpful in detection of methadone-induced encephalopathy.

Measurable residual disease (MRD) assessment using multicolor flow cytometry (MFC) has become the center point of pediatric B‐cell precursor acute lymphoblastic leukemia (BCP‐ALL) risk stratification and therapeutic management. The addition of new markers can improve the accuracy and applicability of MFC‐based MRD assay further. Herein, we evaluated the utility of a new marker, CD304/neuropilin‐1, in the assessment of MFC‐based MRD.

Differentiating glioma recurrence from treatment-related changes can be challenging on conventional imaging. We evaluated the efficacy of quantitative parameters measured by dual-energy spectral computed tomographic (CT) for this differentiation. Twenty-eight patients were examined by dual-energy spectral CT. The effective and normalized atomic number (Zeff and Zeff-N, respectively); spectral Hounsfield unit curve (λHU) slope; and iodine and normalized iodine concentration (IC and ICN, respectively) in the post-treatment enhanced areas were calculated. Pathological results or clinicoradiologic follow-up of ≥2 months were used for final diagnosis. Nonparametric and t-tests were used to compare quantitative parameters between glioma recurrence and treatment-related changes. Sensitivity, specificity, positive and negative predictive values (PPV and NPV, respectively), and accuracy were calculated using receiver operating characteristic (ROC) curves. Predictive probabilities were used to generate ROC curves to determine the diagnostic value. Examination of pre-contrast λHU, Zeff, Zeff-N, IC, ICN, and venous phase ICN showed no significant differences in quantitative parameters (P > 0.05). Venous phase λHU, Zeff, Zeff-N, and IC in glioma recurrence were higher than in treatment-related changes (P < 0.001). The optimal venous phase threshold was 1.03, 7.75, 1.04, and 2.85 mg/cm3, achieving 66.7, 91.7, 83.3, and 91.7% sensitivity; 100.0, 77.8, 88.9, and 77.8% specificity; 100.0, 73.3, 83.3, and 73.3% PPV; 81.8, 93.3, 88.9, and 93.3% NPV; and 86.7, 83.3, 86.7, and 83.3% accuracy, respectively. The respective areas under the curve (AUCs) were 0.912, 0.912, 0.931, and 0.910 in glioma recurrence and treatment-related changes. Glioma recurrence could be potentially differentiated from treatment-related changes based on quantitative values measured by dual-energy spectral CT imaging.

Purpose Arterial spin labeling (ASL) perfusion MRI is a noninvasive technique for measuring cerebral blood flow (CBF) in a quantitative manner. A technical challenge in ASL MRI is data processing because of the inherently low signal-to-noise-ratio (SNR). Deep learning (DL) is an emerging machine learning technique that can learn a nonlinear transform from acquired data without using any explicit hypothesis. Such a high flexibility may be particularly beneficial for ASL denoising. In this paper, we proposed and validated a DL-based ASL MRI denoising algorithm (DL-ASL). Methods The DL-ASL network was constructed using convolutional neural networks (CNNs) with dilated convolution and wide activation residual blocks to explicitly take the inter-voxel correlations into account, and preserve spatial resolution of input image during model learning. Results DL-ASL substantially improved the quality of ASL CBF in terms of SNR. Based on retrospective analyses, DL-ASL showed a high potential of reducing 75% of the original acquisition time without sacrificing CBF measurement quality. Conclusion DL-ASL achieved improved denoising performance for ASL MRI as compared with current routine methods in terms of higher PSNR, SSIM and Radiologic scores. With the help of DL-ASL, much fewer repetitions may be prescribed in ASL MRI, resulting in a great reduction of the total acquisition time.

Lung cancer brain metastases are very common and one of the common causes of treatment failure. We aimed to examine the clinical use of chemical exchange saturation transfer (CEST) technology in the evaluation of brain metastases for lung cancer diagnosis and prognosis. We included26 cases of lung cancer brain metastases, 15 cases of gliomas, and 20 cases with normal tests. The magnetization transfer ratio (MTR;3.5 ppm) image from the GRE-EPI-CEST sequence was analyzed using the ASSET technique and APT technology. The MTR values were measured in the lesion-parenchymal, edema, and non-focus regions, and the MTR image was compared with the conventional MRI. ANOVA and t-test were used for statistical analysis. The lesion-parenchymal, edema, and non-focus areas in the metastatic-tumor-group were red-yellow, yellow-green, and green-blue, and the MTR values were 3.29 ± 1.14%,1.28 ± 0.36%,and 1.26 ± 0.31%, respectively. However, in the glioma-group, the corresponding areas were red, red-yellow, and green-blue, and the MTR values were 6.29 ± 1.58%, 2.87 ± 0.65%, and 1.03 ± 0.30%, respectively. The MTR values of the corresponding areas in the normal-group were 1.07 ± 0.22%,1.04 ± 0.23%, and 1.06 ± 0.24%, respectively. Traditional MR images are in black-white contrast and no metabolic information is displayed. The MTRvalues of the three regions were significantly different among the three groups. The values were also significantly different between the parenchymal and edema areas in the metastatic-tumor-group. There were significant differences in the MTR values between the non-lesion and edema regions, but there was no significant difference between the edema and non-focus areas. In the glioma-group, there were significant differences in the MTR values between the parenchymal and edema areas, between the parenchymal and non-focus areas, and between the edema and non-focus areas. CEST reflects the protein metabolism; therefore, early diagnosis of brain metastases and assessment of the prognosis can be achieved using molecular imaging.

Canines, which exhibit similar emotional and social processing to humans, are becoming one of the preferred animal models for neuroscience research. Beagles are the most common laboratory canine, thanks to their moderate size, docile nature, and strong immunity. However, there is currently no MRI brain template for the purebred Beagle, which hinders their use in studies involving neuroimaging. Here, we present the Beagle Brain Template (BBT), which consists of high-resolution in vivo T1-weighted and T2-weighted templates, as well as a myelin template, generated from purebred Beagles. We also present a normalized pipeline for mapping individual structure images onto the BBT space. The BBT shows low variation in the tissue probability map and provides descriptive statistics with smaller variability of brain tissue volumes and brain sizes than that of existing templates. This high-resolution purebred canine brain template lays the foundation for future studies aimed at in vivo analyses of the brain structure and function of the Beagle dogs.

Purpose High resolution multi-gradient echo (MGE) scanning is typically used for detection of molecularly targeted iron oxide particles. The images of individual echoes are often combined to generate a composite image with improved SNR from the early echoes and boosted contrast from later echoes. In 3D implementations prolonged scanning at high gradient duty cycles induces a B0 shift that predominantly affects image alignment in the slow phase encoding dimension of 3D MGE images. The effect corrupts the composite echo image and limits the image resolution that is realised. A real-time adaptive B0 stabilisation during respiration gated 3D MGE scanning is shown to reduce image misalignment and improve detection of molecularly targeted iron oxide particles in composite images of the mouse brain. Methods An optional B0 measurement block consisting of a 16 μs hard pulse with FA 1°, an acquisition delay of 3.2 ms, followed by gradient spoiling in all three axes was added to a respiration gated 3D MGE scan. During the acquisition delay of each B0 measurement block the NMR signal was routed to a custom built B0 stabilisation unit which mixed the signal to an audio frequency nominally centred around 1000 Hz to enable an Arduino based single channel receiver to measure frequency shifts. The frequency shift was used to effect correction to the main magnetic field via the B0 coil. The efficacy of B0 stabilisation and respiration gating was validated in vivo and used to improve detection of molecularly targeted microparticles of iron oxide (MPIO) in a mouse model of acute neuroinflammation. Results Without B0 stabilisation 3D MGE image data exhibit varying mixtures of translation, scaling and blurring, which compromise the fidelity of the composite image. The real-time adaptive B0 stabilisation minimises corruption of the composite image as the images from the different echoes are properly aligned. The improved detection of molecularly targeted MPIO easily compensates for the scan time penalty of 14% incurred by the B0 stabilisation method employed. Respiration gating of the B0 measurement and the MRI scan was required to preserve high resolution detail, especially towards the back of the brain. Conclusions High resolution imaging for the detection of molecularly targeted iron oxide particles in the mouse brain requires good stabilisation of the main B0 field, and can benefit from a respiration gated image acquisition strategy.

Successful injection of radiolabeled compounds is critical for positron emission tomography (PET) imaging. A poor quality injection limits the tracer availability in the body and can impact diagnostic results. In this study, we attempt to quantify our infiltration rates, develop an actionable quality improvement plan to reduce potentially compromised injections, and compare injection scoring to PET/CT imaging results. A commercially available system that uses external radiation detectors was used to monitor and score injection quality. This system compares the time activity curves of the bolus relative to a control reading in order to provide a score related to the quality of the injection. These injection scores were used to assess infiltration rates at our facility in order to develop and implement a quality improvement plan for our PET imaging center. Injection scores and PET imaging results were reviewed to determine correlations between image-based assessments of infiltration, such as liver SUVs, and injection scoring, as well as to gather infiltration reporting statistics by physicians. A total of 1033 injections were monitored at our center. The phase 1 infiltration rate was 2.1%. In decision tree analysis, patients < 132.5lbs were associated with infiltrations. Additional analyses suggested patients > 127.5 lbs. with non-antecubital injections were associated with lower quality injections. Our phase 2 infiltration rate was 1.9%. Comparison of injection score to SUV showed no significant correlation and indicated that only 63% of suspected infiltrations were visible on PET/CT imaging. Developing a quality improvement plan and monitoring PET injections can lead to reduced infiltration rates. No significant correlation between reference SUVs and injection score provides evidence that determination of infiltration based on PET images alone may be limited. Results also indicate that the number of infiltrated PET injections is under-reported.

Purpose To investigate the correlations between cortical bone microstructural properties and total water proton density (TWPD) obtained from three-dimensional ultrashort echo time Cones (3D-UTE-Cones) magnetic resonance imaging techniques. Materials and methods 135 cortical bone samples were harvested from human tibial and femoral midshafts of 37 donors (61 ± 24 years old). Samples were scanned using 3D-UTE-Cones sequences on a clinical 3T MRI and on a high-resolution micro-computed tomography (μCT) scanner. TWPD was measured using 3D-UTE-Cones MR images. Average bone porosity, pore size, and bone mineral density (BMD) were measured from μCT images at 9 μm voxel size. Pearson's correlation coefficients between TWPD and μCT-based measures were calculated. Results TWPD showed significant moderate correlation with both average bone porosity (R = 0.66, p < 0.01) and pore size (R = 0.58, p < 0.01). TWPD also showed significant strong correction with BMD (R = 0.71, p < 0.01). Conclusions The presented 3D-UTE-Cones imaging technique allows assessment of TWPD in human cortical bone. This quick UTE-MRI-based technique was capable of predicting bone microstructure differences with significant correlations. Such correlations highlight the potential of UTE-MRI-based measurement of bone water proton density to assess bone microstructure.

We sought to enhance the cytometric analysis of myelodysplastic syndromes (MDS) by performing a pilot study of a single cell mass cytometry (MCM) assay to more comprehensively analyze patterns of surface marker expression in patients with MDS.

The Rician noise formed in magnetic resonance (MR) imaging greatly reduced the accuracy and reliability of subsequent analysis, and most of the existing denoising methods are suitable for Gaussian noise rather than Rician noise. Aiming to solve this problem, we proposed fuzzy c-means and adaptive non-local means (FANLM), which combined the adaptive non-local means (NLM) with fuzzy c-means (FCM), as a novel method to reduce noise in the study. The algorithm chose the optimal size of search window automatically based on the noise variance which was estimated by the improved estimator of the median absolute deviation (MAD) for Rician noise. Meanwhile, it solved the problem that the traditional NLM algorithm had to use a fixed size of search window. Considering the distribution characteristics for each pixel, we designed three types of search window sizes as large, medium and small instead of using a fixed size. In addition, the combination with the FCM algorithm helped to achieve better denoising effect since the improved the FCM algorithm divided the membership degrees of images and introduced the morphological reconstruction to preserve the image details. The experimental results showed that the proposed algorithm (FANLM) can effectively remove the noise. Moreover, it had the highest peak signal-noise ratio (PSNR) and structural similarity (SSIM), compared with other three methods: non-local means (NLM), linear minimum mean square error (LMMSE) and undecimated wavelet transform (UWT). Using the FANLM method, the image details can be well preserved with the noise being mostly removed. Compared with the traditional denoising methods, the experimental results showed that the proposed approach effectively suppressed the noise and the edge details were well retained. However, the FANLM method took an average of 13 s throughout the experiment, and its computational cost was not the shortest. Addressing these can be part of our future research.

Objective Diffusion-weighted imaging (DWI) in the liver suffers from signal loss due to the cardiac motion artifact, especially in the left liver lobe. The purpose of this work was to improve the image quality of liver DWI in terms of cardiac motion artifact reduction and achievement of black-blood images in low b-value images. Material and methods Ten healthy volunteers (age 20–31 years) underwent MRI examinations at 1.5 T with a prototype DWI sequence provided by the vendor. Two diffusion encodings (i.e. waveforms), monopolar and flow-compensated, and the b-values 0, 20, 50, 100, 150, 600 and 800 s/mm2 were used. Two Likert scales describing the severity of the pulsation artifact and the quality of the black-blood state were defined and evaluated by two experienced radiologists. Regions of interest (ROIs) were manually drawn in the right and left liver lobe in each slice and combined to a volume of interest (VOI). The mean and coefficient of variation were calculated for each normalized VOI-averaged signal to assess the severity of the cardiac motion artifact. The ADC was calculated using two b-values once for the monopolar data and once with mixed data, using the monopolar data for the small and the flow-compensated data for the high b-value. A Wilcoxon rank sum test was used to compare the Likert scores obtained for monopolar and flow-compensated data. Results At b-values from 20 to 150 s/mm2, unlike the flow-compensated diffusion encoding, the monopolar encoding yielded black blood in all images with a negligible signal loss due to the cardiac motion artifact. At the b-values 600 and 800 s/mm2, the flow-compensated encoding resulted in a significantly reduced cardiac motion artifact, especially in the left liver lobe, and in a black-blood state. The ADC calculated with monopolar data was significantly higher in the left than in the right liver lobe. Conclusion It is recommendable to use the following mixed waveform protocol: Monopolar diffusion encodings at small b-values and flow-compensated diffusion encodings at high b-values.

Differences in brain morphology across population groups necessitate creation of population-specific Magnetic Resonance Imaging (MRI) brain templates for interpretation of neuroimaging data. Variations in the neuroanatomy in a genetically heterogeneous population make the development of a population-specific brain template for the Indian subcontinent imperative. A dataset of high-resolution 3D T1, T2, and FLAIR images acquired from a group of 113 volunteers (M/F - 56/57, mean age 28.96 ± 7.80 years) are used to construct T1, T2, and FLAIR templates, collectively referred to as Indian Brain Template, “BRAHMA”. A processing pipeline is developed and implemented in a MATLAB based toolbox for template construction and generation of tissue probability maps and segmentation atlases, with additional labels for deep brain regions such as the Substantia Nigra generated from the T2 and FLAIR templates. The use of BRAHMA template for analysis of structural and functional neuroimaging data from Indian participants provides improved accuracy with statistically significant results over that obtained using the ICBM-152 (International Consortium for Brain Mapping) template. Our results indicate that segmentations generated on structural images are closer in volume to those obtained from registration to the BRAHMA template than to the ICBM-152. Furthermore, functional MRI data obtained for Working Memory and Finger Tapping paradigms processed using the BRAHMA template shows a significantly higher percentage of the activation area than ICBM-152 in relevant brain regions, i.e. the left middle frontal gyrus, and the left and right precentral gyri, respectively. The availability of different image contrasts, tissue maps, and segmentation atlases makes the BRAHMA template a comprehensive tool for multi-modal image analysis in laboratory and clinical settings.

Excerpt: This month, we shift our format to listen in on the conversation of three legends of immunology. Sir Marc Feldmann, Lasker awardee in 2003 for his role in discovering anti-TNF therapy, acts as interviewer, speaking with the two winners of the 2019 Albert Lasker Basic Medical Research Award: Max D....

The 2019 Nobel Prize for Physiology or Medicine was awarded to Professors Sir Peter J. Ratcliffe (University of Oxford), Gregg L. Semenza (Johns Hopkins University), and William G. Kaelin Jr. (Dana-Farber Cancer Institute) for their discoveries of a fundamental aspect of cellular physiology, the cellular sensing of oxygen levels and regulation of physiologic hypoxia. Each of these physician-scientists was intrigued by a different clinically relevant observation and utilized very basic biochemical tools to address their questions. These separate lines of investigation converged, delineating a central cellular pathway with far-ranging implications for human physiology, disease states, and medicine. The story of how they uncovered hypoxia response begins with a deep interest in basic human biology. Uncovering a hypoxia-inducible pathway Semenza, a pediatric geneticist, was studying the triggers for the production of erythropoietin, a hematopoietic growth factor produced by the liver and kidney that promotes the generation of red blood cells. His group identified a sequence-specific binding site (termed hypoxia-response element [HRE]) for a transcription factor in the 3′ flanking region of the human erythropoietin gene (EPO). He biochemically purified the factor, which he called hypoxia-inducible factor 1 (HIF-1) (1). HIF-1 is a heterodimer composed of HIF-1α, a protein expressed in an oxygen-regulated manner, and a constitutively expressed factor, HIF-1β. This dimer formed a potent transcription factor complex, and Semenza showed that in addition to erythropoietin, HIF-1 induces a number of other genes that are critical for cellular and systemic response to hypoxia, and maintenance of cellular homeostasis. Among these was vascular endothelial growth factor (VEGF), which plays important roles in angiogenesis (2). A cancer connection Simultaneously, Kaelin was studying von Hippel–Lindau (VHL) disease, a rare genetic syndrome in which mutations in the affected gene (VHL) lead to specific cancer types, such as renal cell carcinoma (RCC) and cerebellar hemangioblastomas. Trained as an internist (he was chief resident of the Johns Hopkins Osler service) and oncologist, he was intrigued by VHL syndrome because the associated tumors were always highly vascular in nature, with affected patients occasionally having secondary polycythemia. Pivotal biochemical studies showed that the protein product of VHL (pVHL) forms a complex that plays an important role in the ubiquitination and subsequent degradation of specific proteins. Importantly, the proper assembly of the VHL complex was critical for regulation of hypoxia-inducible genes (3). X-ray crystallography of the VHL complex suggested that pVHL serves as an E3 ubiquitin ligase, conferring specificity to the ubiquitination and subsequent degradation of one or more proteins (4). The quest to find the protein was on. Putting the pieces together A crucial observation connecting these lines of research came from the Ratcliffe group. Ratcliffe, a nephrologist, was intrigued by how kidneys serve as oxygen-sensing organs and thus regulate the production of erythropoietin systemically. In early experiments, his group showed that multiple cell types are capable of sensing hypoxia and driving EPO transcription via the HRE that Semenza had identified (5). This suggested that HIF possibly serves as a universal response mechanism to hypoxia. Importantly, in 1999, the Ratcliffe team showed that pVHL regulates HIF-1α and most likely acts as its E3 ubiquitin ligase (6). Regulating the VHL-HIF interaction The mechanisms underpinning HIF-1α stabilization and activation of a massive transcriptional program of hypoxia response were elegantly delineated by the Kaelin, Semenza, and Ratcliffe groups, revealing a beautifully simple model. During normoxia, when oxygen is ample, specific proline residues on HIF-1α undergo hydroxylation. This covalently modified form of HIF-1α is recognized in a contact-dependent manner by pVHL, marking HIF-1α for ubiquitination and proteasome-mediated destruction. During hypoxia, HIF-1α is not hydroxylated and escapes tagging for degradation (7, 8). This suggested that regulation of HIF is posttranscriptional: HIF-1α is transcribed, translated, and quickly degraded, unless oxygen becomes limiting. Notably, a second homologous protein, HIF-2α, was identified, featuring identical hydroxylation-dependent regulation via VHL. HIF-1/2α, when stabilized, rapidly heterodimerizes with HIF-1β, transcribing hundreds of genes that are critical for the cellular response to hypoxia. The genes involved in this tightly controlled response pathway include notable heavyweights such as VEGF, erythropoietin, mediators of glycolysis and other metabolic pathways, and genes involved in cell survival and homeostasis — and new target genes continue to be uncovered. Knowing the importance of hydroxylation in the recognition of HIF-1α by pVHL, the hunt to identify the responsible enzymes began. Prolyl hydroxylation had been well defined in the setting of stabilization of procollagen chains. There were striking similarities; both reactions required oxygen, iron, and ascorbate, and were inhibited by cobalt and by 2-oxoglutarate analogs, suggesting that the HIF prolyl hydroxylase was a member of the 2-oxoglutrate–dependent dioxygenase enzyme family. A group of enzymes were identified as the key oxygen sensors based on the discovery of the egl9 protein in Caenorhabditis elegans: the EglN (Egl nine homolog), or PHD (prolyl hydroxylase domain), proteins. These three orthologs catalyze hydroxylation of human HIF-1/2α (9–11). EglN1 (also called prolyl hydroxylase domain–containing protein–2 [PHD2]) was shown to be the critical hydroxylase for HIF-α in vivo (12). The requirement for 2-oxoglutate for the reaction provided an additional link between hypoxia and metabolism. EglNs’ unusual low oxygen affinity suggested that these molecules were indeed oxygen sensors, an observation that was confirmed genetically. In murine models in which EglN1 is temporally genetically deleted, mice display hypervascular features and polycythemia (12). The phenotype of these mice mimicked responses to high altitude. Further, inactivating mutations in EglN1 or activating mutations in HIF-2α have been shown to cause familial erythrocytosis (13, 14). Even more intriguing, single nucleotide polymorphisms (SNPs) or missense mutations in EglN1 allow for high-altitude adaptation in populations living in high altitudes (e.g., Tibet) (15). Hypoxia in the patient setting Let’s put the discoveries of hypoxia response in context with a clinical case: A middle-aged woman was admitted to the hospital with pathologic fracture of the femur as a result of metastatic clear cell RCC. Past medical history was significant for coronary artery disease, and she had mild cardiomyopathy. A smoker, she had chronic kidney disease and anemia. Hypoxia signaling played a central role in nearly every feature of her disease process, providing for an outstanding teaching opportunity with the house staff team. This patient’s cancer is likely driven by inactivation of the VHL gene. She had been treated for 11 months with a VEGFR inhibitor, with good disease control. The model proposed by which VHL loss resulted in stabilization of HIF factors and transcriptional activation of hypoxia-associated genes immediately explained why VHL syndrome–associated cancers were hypervascular. Somatic mutations in VHL are tightly linked to sporadic clear cell RCC. Not surprisingly, clear cell RCC is one of the select groups of cancers for which VEGF pathway–directed therapy (Figure 1) has been proven to induce substantial responses in tumor volume and an increase in overall survival (16). This discovery can be directly linked to the emergence of a class of drugs targeting VEGF signaling that have become a staple of the cancer targeted therapy armamentarium. Figure 1 The discovery of the VHL/EglN/HIF pathway as a central mediator of hypoxia signaling has paved the way for introduction of drugs that modulate the pathway for the treatment of human disease. Because the pathway is so central to so many pathological conditions, pharmacologics are being used for the treatment of cancer, as well as being tested for other conditions, such as anemia and cardiovascular and pulmonary diseases. Therapeutics targeting this pathway include VEGF pathway inhibitors (bevacizumab, sorafenib, sunitinib, pazopanib, axitinib, cabozantinib, and lenvatinib), mTOR inhibitors (temsirolimus and everolimus), EglN inhibitors in phase III trials (daprodustat, molidustat, roxadustat, and vadadustat), and investigational HIF-2α inhibitors (PT2385, PT2977, and RNAi [phase I]). Critical for our patient, the physiologic and chronic response to hypoxia resulting from coronary artery disease, damaged lung epithelium, and recurrently injured kidneys plays important roles in tissue remodeling and disease states. VEGFR inhibition may have potentially contributed directly to microvascular dysfunction, myocardial hypoxia, and (ironically) stabilization of HIF in myocytes and subsequent myocardial dysfunction (17). Hypoxia signaling alters the metabolic properties of these tissues, shifts the balance of reactive oxygen species, and accumulates free radical–induced damage. Hypoxia-mediated effects can impact any tissue in which delivery of oxygen and nutrients is critical, wherein hypoxia signaling underlies serious nonmalignant and malignant conditions. The bone marrow and kidneys are worthy of special consideration in this case. Hypoxic signaling acts as a rheostat that maintains the necessary growth signals for stem cells. The bone marrow niche is where blood stem cells reside, and perturbations — such as infiltration with cancer cells, fractures and disrupted blood flow, and radiation exposure — have the potential to damage this critical space. Similarly, cells with exquisite sensory capacity, predominately localized in the kidney, utilize HIF signaling to maintain erythropoietin production that stimulates erythroid precursor differentiation in that marrow niche. End organ damage at either site can significantly impact a patient’s ability to keep up with demand for red cell production. Conclusions The discoveries by Semenza, Kaelin, and Ratcliff began with a keen focus on fundamental aspects of human physiology: signaling that alters red blood cell production and ultimately oxygen carrying capacity, and the vasculature that delivers that essential cargo. In the realm of cancer, while VHL-associated tumors and RCC display a remarkable pseudohypoxic state and vascular dependence due to constitutive stabilization of HIF-2α, in many other tumor types one or both HIF factors are stabilized or upregulated, which can frequently be a potent biomarker of aggressive tumors. Importantly, small molecules that target HIF proteins are emerging as cancer therapeutics (18). As a result of these seminal discoveries, therapies that dampen hypoxic response have also been applied or tested in other settings, including retinal diseases, pulmonary hypertension, cardiovascular disease, renovascular disease, and immune regulation. Conversely, therapies are being developed that apply a precision approach to selectively stabilize HIF, inhibiting the EglN/HIF axis as a treatment for patients with chronic anemia and chronic kidney disease (19), bringing the original observations full circle. The three physician-scientists honored with the 2019 Nobel Prize in Physiology or Medicine highlight the tight coupling between clinical observations and fundamental aspects of human biology, inspire future physicians to apply that level of attention to clinical medicine, and pave the way for innovative therapeutic advances through their unwavering pursuit of basic research into the mechanisms by which cells sense and respond to oxygen. Acknowledgments JM is supported by NIH R56 HL141466 and R01 HL141466. WKR is supported by R01 CA198482 and R01 CA203012. Footnotes Conflict of interest: JM has served on an advisory boards for Pfizer, Novartis, Bristol-Myers Squibb, Audentes Therapeutics, Nektar, and AstraZeneca. WKR serves on the Board of Scientific Advisors for the National Cancer Institute, and on the scientific advisory board for Aravive. 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Sickle cell disease (SCD) is a heritable disorder of hemoglobin that affects 1 of every 400 black newborns and approximately 100,000 persons in the United States (1). This disease burden has a considerable impact on individuals affected and on health care systems. In the United States alone, the medical cost of caring for patients with SCD exceeds $1 billion annually. SCD is caused by a point mutation in codon 6 of the β-globin chain that results in an amino acid substitution of valine for glutamic acid, and promotes the formation of long hemoglobin polymers under hypoxic conditions. This abnormal polymerization deforms erythrocytes and causes significant alterations in red cell integrity, rheologic properties, and lifespan. SCD leads to chronic hemolysis and a vasculopathy that involves virtually every organ. Most adults and many children develop a chronic, debilitating condition, leading to high rates of disability and unemployment. A current cohort of adults that were followed and treated with disease-modifying therapy at two large academic medical centers had a median survival of 48 years (2), which is not much different when compared with a NIH-sponsored multicenter, prospective study of a cohort of adults with SCD that was published 25 years ago (3). Allogeneic blood or marrow transplantation (alloBMT) is the only cure for patients with sickle cell disease (SCD) (4). Worldwide, nearly 2000 children and adults with SCD have received alloBMT (5). Depending on the type of transplant and donor source, the cure rate is 90%–95%, and the risk of graft-versus-host disease (GVHD) is 4%–15% in the United States and Europe. Most of these data are from pediatric studies involving myeloablative conditioning regimens and stem cell grafts from matched sibling donors. Adult patients with SCD are often excluded from myeloablative BMT trials because of projected excess morbidity and mortality resulting from accumulated end-organ damage from decades of living with SCD. Additionally, many parents of children or affected individuals with SCD are reluctant to allow or receive myeloablative conditioning because of the nearly universal gonadal failure. Finding suitable donors has also been challenging. HLA-matched sibling donors are available in less than 15% of potential alloBMT recipients with SCD. Less than a quarter of African Americans have HLA matches in unrelated registries (6). Accordingly, broad application of alloBMT in SCD is dependent on novel strategies that address donor availability and limit toxicity from myeloablative conditioning regimens and GVHD. These limitations of donor availability and GVHD are driving research for novel approaches to BMT that use autologous cells with gene therapy or gene editing (Figure 1). Figure 1 Curative approaches to SCD. (A) Gene therapy requires the harvesting of HSPCs from the patient, transduction of these cells with a nonsickling viral vector, and myeloablative chemotherapy followed by autologous BMT. (B) Gene editing also requires the harvesting of HSPCs from the patient. Gene editing of HSPCs is accomplished with electroporation of gene-editing reagents, followed by myeloablative conditioning and autologous BMT using the gene-corrected cells. (C) alloBMT can be from an HLA-matched sibling donor, a matched unrelated donor, or an HLA-haploidentical family donor. Bone marrow is harvested from a healthy donor. Traditionally, patients received myeloablative chemotherapy, but in recent years nonmyeloablative therapy, especially for HLA-haploidentical BMT with post-transplantation cyclophosphamide, has become more common. Healthy donor HSPCs are infused, followed by post-transplantation administration of cyclophosphamide to prevent GVHD and graft rejection. Children with strokes and adults with severe heart, lung, or kidney disease or strokes are typically excluded from gene therapy trials but are eligible to participate in the NIH-supported HLA-haploidentical BMT with post-transplantation cyclophosphamide phase II trial (NCT03263559). Myeloablative gene therapy for SCD Gene therapy involves the harvesting of hematopoietic stem/progenitor cells (HSPCs), ex vivo transduction using a retroviral vector carrying a γ-globin or β-globin transgene, and reinfusion of transduced HSPCs following myeloablative chemotherapy. Since HSPCs are patient derived, there is no risk of GVHD; however, myeloablative chemotherapy (usually with busulfan) is required to reduce or eliminate host hematopoiesis. Myeloablative chemotherapy leads to infertility, alopecia, mucositis, and infections and may exclude patients with moderate-to-severe end-organ damage due to dose-limiting toxicities from busulfan. Stroke, a major source of morbidity, is an exclusion criterion for most gene therapy trials. There is also the potential for secondary malignancies from insertional mutagenesis and from busulfan. Self-inactivating lentiviral vectors mitigate, but do not eliminate, the risk for insertional mutagenesis. Furthermore, busulfan is seldom 100% myeloablative, and surviving HSPCs may also lead to late myeloid malignancies. Mobilizing enough HSPCs from patients with SCD and collecting enough self-renewing HSPCs to allow life-long expression of the transgene is also a challenge. Stem cell mobilization with granulocyte CSF (G-CSF) is contraindicated in SCD; therefore, current trials are using bone marrow harvesting, which is especially painful for patients with SCD and may still result in insufficient HSPC yields for successful BMT. Plerixifor mobilization is under investigation, and early results appear promising (7). Ensuring sufficient transduction of HSPCs to allow long-term engraftment is more problematic. Lentiviral vectors can transduce self-renewing G0 stem cells required for long-term transgene expression; however, the majority of transduced cells following peripheral blood mobilization are progenitor cells with limited to no self-renewal capacity. Progenitor cells survive three to four months and generate red cells that survive for 120 days. Moreover, autologous recovery following BMT leads to increased fetal hemoglobin that can decrease acute vaso-occlusive episodes for a year or more after BMT (8); thus, follow-up beyond two years is necessary to ensure that the transduced HSPCs are stable and sufficient to lead to long-term control of the disease. Despite these limitations, preliminary results of gene therapy for SCD and severe β-thalassemia are encouraging, with the largest experience in severe β-thalassemia (9). In two phase I–II studies of gene therapy using a lentiviral vector and myeloablative busulfan conditioning, 12 of 13 patients with a non-β0/β0 genotype achieved transfusion independence, with a median follow-up of over two years. In nine patients with the β0/β0 genotype, transfusion requirements decreased, but just three of nine were able to discontinue transfusions. The first successful case report of a patient with SCD treated with gene therapy was in 2017 (10). At the time of the report, the child was 15 months from having received his transplant and no longer experiencing vaso-occlusive crises. Of note, one of two additional patients treated in the same clinical trial benefitted from the therapy. Another exciting approach to gene therapy in clinical trials is to increase production of fetal hemoglobin by knockdown of BCL11A, a gene whose product, BCL11A, regulates hemoglobin F expression. Reducing BCL11A thus increases the amount of nonsickling γ-globin. A number of other clinical trials involving gene therapy to treat SCD are underway. Initial data should be available within the next two to three years, but long-term data of at least five- and ten-year intervals are necessary to address late graft failure and other late effects. Myeloablative gene editing for SCD The approach to gene editing is similar to that for gene therapy and involves the harvesting of HSPCs, ex vivo electroporation of target cells to correct the β-globin gene or to knock down BCL11A using CRISPR/Cas9 or zinc finger nucleases, and reinfusion of genetically modified HSPCs following myeloablative chemotherapy. The toxicities and limitations from mobilization and myeloablative chemotherapy are identical to those for gene therapy protocols. No retroviral transduction is needed, but recent data on CRISPR/Cas9 editing show that the frequency of large deletions and insertions that arise near the on-target site is higher than originally thought (11). Moreover, since DNA breaks induce apoptosis in healthy cells, it appears that there is enrichment of edited HSPCs with deficient p53, raising additional safety concerns regarding cancer risk (12). Nonmyeloablative haploidentical BMT for SCD The approach to nonmyeloablative haploidentical BMT was developed to increase donor availability and to provide curative options for adults with SCD who have preexisting heart, lung, and kidney dysfunction that would preclude myeloablative therapy. For children and adults with SCD, multiple previous unsuccessful single-center nonmyeloablative, haploidentical BMT protocols were initiated and abandoned because of transplant-related mortality. However, the more recent generation of nonmyeloablative, HLA-haploidentical BMT with post-transplantation cyclophosphamide, roughly one-third the cost of myeloablative gene therapy and gene editing, has dramatically improved the clinical outcome of children and adults with SCD. Virtually every patient eligible for a gene therapy or gene editing trial is also eligible for an HLA-haploidentical BMT with post-transplantation cyclophosphamide. Transplantation trials are more inclusive in that most gene therapy trials exclude patients who have had a stroke. The first clinical trial of nonmyeloablative, HLA-haploidentical BMT with post-transplantation cyclophosphamide for SCD in 2012 reported a graft failure rate of approximately 40% (13); however, subsequent modifications to the preparative regimens involving the addition of thiotepa or an increase in the dose of total body irradiation from 200 cGy to 400 cGy increased engraftment to 90% without adding to toxicity (14–16). The collective results from these three recent studies (n = 39 patients with SCD) showed no mortality, an engraftment rate of 90%, and a rate of GVHD above grade 2 of 8%. A clinical trial sponsored by the National Heart, Lung, and Blood Institute (NHLBI) involving HLA-haploidentical BMT with post-transplantation cyclophosphamide for SCD at more than 30 clinical centers throughout the United States and Europe is currently underway (NCT03263559). Confirmation of these encouraging early results will confirm that myeloablative conditioning and full-matched HLA donors are no longer necessary to cure SCD. Are genetic approaches still necessary to cure SCD? The era of curative therapy for patients with SCD is upon us. NIH-sponsored nonmyeloablative, HLA-haploidentical BMT with post-transplantation cyclophosphamide offers the opportunity to cure up to 95% of the children and 90% of the adults with severe SCD. Clinical trials involving myeloablative gene therapy and genome editing are also underway with 100% donor availability but are limited predominantly to children who can tolerate the myeloablative regimen. Although randomized, controlled trials comparing the two strategies are not likely to be undertaken, understandably, curative therapies that include nonmyeloablative methods will commonly be selected over those that are myeloablative. Informed families with SCD have multiple options to enroll in clinical trials designed to cure and advance care for the next generation. The pressing challenges are to include full disclosure of the various curative options for children and adults with SCD, to minimize late effects from preparative regimens, and to advance innovative science leading to nonmyeloablative, haploidentical BMT, gene therapy, or gene-editing trials. The future for curing children and adults with SCD looks bright. Footnotes Conflict of interest: The authors have declared that no conflict of interest exists. Copyright: © 2020, American Society for Clinical Investigation. Reference information: J Clin Invest. 2020;130(1):7–9. https://doi.org/10.1172/JCI133856. 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The opioid epidemic, now in its second decade, is one of the most challenging public health crises in the US. Providing an effective response is complicated by multiple underlying causes and consequences as well as a misunderstanding of addiction and the medications used to treat it (1). Indeed, medications for opioid use disorder (MOUDs) are the most effective interventions for treating opioid addiction, but are not prescribed to many who would benefit. Here, we describe the distinction between physical dependence and addiction along with its implication for treatment, and discuss the mechanisms of action of MOUDs. Opioid withdrawal versus opioid dependence Opioid use disorder (OUD) is defined as a pattern of maladaptive opioid use that leads to significant impairment or distress. Severity is classified on the basis of the number of symptoms (Table 1) present: mild (one or two), moderate (three or four), and severe (six or more) (2). In this description, opioid addiction corresponds to moderate and severe OUD. Table 1 DSM-5 criteria for diagnostic criteria OUD In diagnosing OUD, many confuse opioid physical dependence with OUD, yet this distinction is crucial for selecting treatment. Physical dependence develops rapidly and occurs in most people who are given repeated doses of opioid medications and manifests as the emergence of acute withdrawal symptoms following discontinuation of opioid drugs. When physical dependence is associated with tolerance, it can lead to a diagnosis of mild OUD (two of the criteria in Table 1). Note that physical dependence and tolerance will be present in many pain patients who are properly treated with opioid medications; hence, the distinction from mild OUD requires the clinician to assess whether significant impairment or distress is present. Physical dependence and the associated acute withdrawal symptoms are adaptations that recover rapidly (within days) and can be managed by slowly tapering the opioid drug without the need of maintenance on opioid medications (3). In contrast, opioid addiction develops in less than 10% of those exposed repeatedly to opioids and is the result of neuroplastic adaptations in brain circuits underlying reward and motivation, self-regulation and decision-making, and mood and stress reactivity that are long lasting, persisting years after drug discontinuation (4, 5). Opioid addiction significantly benefits from the use of medications for OUD. Abrupt cessation of opioids after repeated use can produce an intense but rarely life-threatening withdrawal syndrome, which can be understood as an adaptation to maintaining homeostasis or allostatic process (3). Common symptoms of early withdrawal include mydriasis, piloerection, muscle twitching, lacrimation, rhinorrhea, diaphoresis, yawning, tremor, insomnia, restlessness, myalgia, arthralgia, diarrhea, and nausea or vomiting. As withdrawal progresses, tachycardia, tachypnea, hypertension or hypotension, and dehydration can appear. Note that this is distinct from the protracted withdrawal syndrome characterized by dysphoria, craving, and insomnia that reflects brain circuitry neuroadaptations associated with addiction. Symptoms of acute withdrawal (as well as protracted withdrawal) can be a powerful trigger for relapse for individuals with OUD (1), but can also lead to opioid seeking in pain patients in whom acute opioid withdrawal is not properly managed. Multiple neuroadaptations underlie physical dependence (6), including desensitization and internalization of the μ-opioid receptor (MOR), impaired MOR signaling with intracellular effectors, intracellular upregulation of cAMP/PKA in opioid-sensitive neurons, adaptations in neuropeptide systems that interact with μ-opioid–sensitive neurons, and activation of glial signaling (7). Hyperactivity of the locus coeruleus (LC) underlies many of the symptoms of acute withdrawal, and α1 adrenergic agonists, such as lofexidine and clonidine, which reduce noradrenergic release, are useful for the management of acute opioid withdrawal. In contrast to withdrawal, which is a physiological response to the abrupt decline in MOR occupancy and signaling, addiction is predominantly a disorder of brain circuits that impairs motivation, self regulation, and hedonic tone. The brain mechanisms underlying addiction include the following (3): (a) reward circuitry, originating in the dopamine neurons in the ventral tegmental area and projecting to the nucleus accumbens, ventral prefrontal cortex, and amygdala; (b) emotional circuitry, including the hippocampus, extended amygdala, lateral habenula, dorsal raphe, and insula; and (c) executive control circuitry, which involves widely distributed and complex prefrontal cortex–subcortical circuitry (3). In addition, circuitry involved in interoception modulates awareness of drug-conditioned cues, stress, and negative emotional states (3). Disruption of these circuits underlies the compulsive pattern of drug taking despite its adverse consequences (8). MOUDs MOUDs are the standard of care for OUD (9). They are associated with reduced risk of relapse, overdose deaths, infections, and criminal behavior and are more cost-effective than no OUD treatment or treatment with no medication. There are three medications approved by the FDA for the treatment of OUD: methadone (full MOR agonist), buprenorphine (partial MOR agonist, κ-opioid receptor [KOR] antagonist, and nociceptor receptor agonist), and naltrexone (MOR and KOR antagonist). The MOR is both the therapeutic target for MOUDs and the target for heroin and other opioids when misused for their rewarding effects. For this reason, many have dismissed agonist medications (methadone and buprenorphine) as only substituting one drug for another; however, this view ignores fundamental differences between drugs of abuse and MOUDs. These distinctions include differences in pharmacokinetics, pharmacological effects at the MOR, and doses and routes of administration. Pharmacokinetics and route of administration. The rate at which opioid drugs enter the brain and bind to the MOR modulates their rewarding effects such that drugs with fast uptake into the brain and that interact rapidly with the MOR, such as heroin and fentanyl, are the most rewarding. The route of administration also affects pharmacokinetics; intravenous or smoking administration results in faster brain delivery than taking orally. When used therapeutically, MOUDs are either given orally or in slow-release formulations, which slows the rate of brain entry and clearance. The relatively slow brain clearance of buprenorphine and, to a lesser extent, methadone leads to milder severity of withdrawal upon their discontinuation than when discontinuing heroin or fentanyl. In this respect, buprenorphine leads to a milder withdrawal than methadone. Additionally, the slower pharmacokinetics of MOUDs result in more stable levels of MOR occupancy than misuse of opioid drugs for their rewarding effects. Stable occupancy of MOR by MOUDs controls opioid craving and prevents the emergence of acute withdrawal symptoms. Doses and frequency of administration also differ when opioid drugs are misused for their rewarding effects than when used therapeutically. Methadone is typically injected when it is misused. In the case of buprenorphine, its injection is limited by the combination with the antagonist opioid drug naloxone (Suboxone formulation), which has very poor bioavailability when given sublingually, but if injected, will trigger an acute withdrawal. Nonetheless, there are multiple reports of diversion and misuse of buprenorphine, though it appears that misuse of buprenorphine is mostly to alleviate opiate withdrawal or achieve abstinence from other opioids, particularly when access to this medication is restricted (10). Though MOR is the target for the rewarding and analgesic effects of opioids, the KOR is implicated in the aversive negative emotional states associated with addictions. Preclinical data indicate an upregulation of KOR signaling in animal models of addiction that, when blocked, prevents relapse into drug taking (11). Hence, a priority in addiction treatment has been the development of κ antagonist medications. In this respect the KOR antagonist effects of buprenorphine and naltrexone are likely to contribute to their therapeutic effects. Additionally, buprenorphine also binds to the nociceptin receptor where its agonist effects could also contribute to its efficacy in OUD (12). Which MOUD to use Although there are no empirically based predictors for selecting a specific MOUD, expert consensus and qualitative studies suggest that the selection should be based on the patient’s response to prior treatment with MOUDs, their level of physical dependence, the presence of coexisting conditions, and the patient’s preference (9). Often, the selection is determined by what is available in a given treatment program. Increasingly, however, there is recognition that patients might respond better to a particular MOUD depending on their characteristics and that optimal medication may be different during treatment initiation than stabilization. Methadone has been available for more than 50 years and has the largest evidence of efficacy (13). Methadone would be indicated in patients with severe tolerance in whom buprenorphine treatment might trigger withdrawal symptoms. In general, there is overall better retention with methadone than buprenorphine and higher methadone doses up to 100 mg/day are associated with better outcomes than lower doses (14). As a full agonist, methadone has no ceiling effect, which increases risk for overdoses when used at doses above the patient’s tolerance or when combined with other central nervous depressants such as alcohol, benzodiazepines, heroin, or other synthetic opioids. Methadone is administered daily in an oral formulation. In the US methadone must be administered in licensed outpatient treatment programs (OTPs), which constitutes an important barrier to treatment to many patients, though it might improve outcomes in individuals who benefit from daily behavioral intervention given in OTPs (1). There is interest in exploring expanded access to methadone, such as office-based or via pharmacies (15), and developing extended release formulations of methadone to improve adherence, minimize diversion, and facilitate use in healthcare or justice settings. Buprenorphine has been available to treat OUD for almost two decades (13). Buprenorphine is prescribed in medical offices by clinicians who require a waiver to do so. There are currently 102,570 waivered clinicians in the US, though many are not treating OUD patients (16). Buprenorphine requires daily or every other day dosing, and typical doses range between 8 to 24 mg, with a recommended target dose of 16 mg. Optimal responses to buprenorphine have been obtained in OUD patients with depressive symptoms, which might reflect in part the mood-enhancing effect of KOR antagonists. As a partial MOR agonist, buprenorphine can precipitate acute withdrawal in individuals with OUD who use high doses of heroin or fentanyl or have been maintained on high doses of methadone. In those instances, it might be best to initiate treatment with methadone and, after slowly tapering the dose, continue with buprenorphine. Buprenorphine is less likely to induce respiratory depression than methadone, but it can still be lethal when combined with other central nervous depressant substances (17). Extended-release (XR) formulations of buprenorphine were recently developed that include an FDA-approved six-month implant, a one-week formulation that is being reviewed by the FDA, and one-month formulations of buprenorphine, one of which was already approved by FDA (1). Limited data are available regarding the acceptability and efficacy of these new formulations in OUD. Naltrexone is a MOR antagonist, but the utility of the immediate release formulation for OUD treatment has been limited by poor adherence. The development of a monthly XR–extended release naltrexone (XR-NTX) formulation significantly improved treatment retention and outcomes (18). Naltrexone is an antagonist drug that triggers acute withdrawal if OUD patients are not detoxified prior to induction. Current recommendations are for patients to be abstinent for one week prior to XR-NTX induction, which constitutes a barrier to induct some patients into treatment. Some protocols have been developed for faster supervised medical withdrawal (formerly known as detoxification), but further research is needed before adoption in routine clinical practice. The KOR antagonist effects could contribute to the mood improvements reported in OUD patients treated with naltrexone. Presence of cooccurring disorders may be another consideration in MOUD selection. For example, naltrexone is also effective for alcohol dependence so comorbid OUD with alcoholism might benefit uniquely from this medication, whereas the KOR antagonist properties of buprenorphine may offer unique benefits for OUD patients with comorbid depression. For pregnant women, methadone or buprenorphine is recommended, due to insufficient data on safety of naltrexone. Conclusion MOUDs are among the most effective interventions for preventing overdose mortality and improving outcomes in patients with OUD. However, stigmatization and lack of understanding of addiction and the medications used to treat OUD have interfered with their implementation. The increased recognition that MOUDs are crucial for controlling the current opioid crisis highlights the importance of engaging healthcare in the screening and treatment of OUD. The views and opinions expressed in this report are those of the authors and should not be construed to represent the views of any of the sponsoring organizations or agencies or the US government. Footnotes Conflict of interest: The authors have declared that no conflict of interest exists. Copyright: © 2020, American Society for Clinical Investigation. Reference information: J Clin Invest. 2020;130(1):10–13. https://doi.org/10.1172/JCI134708. References Blanco C, Volkow ND. Management of opioid use disorder in the USA: present status and future directions. Lancet. 2019;393(10182):1760–1772.View this article via: PubMedCrossRefGoogle Scholar American Psychiatric Association. Diagnostic and Statistical Manual of Mental Disorders. 5th ed. Washington, DC, USA: American Psychiatric Publishing; 2013. Koob GF, Volkow ND. Neurobiology of addiction: a neurocircuitry analysis. Lancet Psychiatry. 2016;3(8):760–773.View this article via: PubMedCrossRefGoogle Scholar Kalivas PW, Volkow ND. 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The increasing availability of DNA sequence data and access to sophisticated bioinformatic algorithms mean that an unbiased bioinformatics-based assessment of the predicted impact of a genomic variant is rapidly available. The key point of this Viewpoint article is that such bioinformatic assessments are not equivalent to an expert diagnostic interpretation and may be misleading in both research and clinical care. Predication algorithms in genomic medicine Recently published examples involving monogenic diabetes demonstrate how pathogenicity prediction algorithms can be very inaccurate for predicting which genetic variants are likely causal of dominant monogenic disease (1–4). Here, we highlight the potential pitfalls of variant classification and how they can be avoided. A recent study used a bioinformatic algorithm to identify 88 “likely pathogenic” monogenic diabetes variants in 80 individuals (8.6%) from a cohort of 1019 individuals with type 1 diabetes for 50 or more years (4). Application of the widely used American College of Medical Genetics and Genomics and the Association for Molecular Pathology (ACMG/AMP) standards and guidelines (5) classifies only nine of these 88 variants as likely pathogenic or pathogenic variants that would be reported by our clinical diagnostic laboratory as likely causative of the patients’ diabetes. This is not an isolated occurrence; other published research studies with an overreliance on in silico prediction tools have reported high levels (~90%) of false positive “likely pathogenic” monogenic diabetes variants (1–3). We have seen clinical diagnostic reports from laboratories in eight countries across Europe, Asia, the Middle East, and the United States that have similarly reported such variants as incorrectly likely causative of a patient’s diabetes. Such great discrepancies occur not because the bioinformatic algorithm is wrong, or even based on incorrect scientific principles, but because variant interpretation in the clinical setting requires other information in addition to the predicted effect upon protein function. This additional information includes knowledge regarding the gene-disease validity, mode of inheritance, appropriate allele frequency cutoff thresholds, most clinically relevant transcript, and specificity of disease-causing variant type for each gene. Each of these is discussed in turn below and illustrated in Figure 1. Figure 1 Flowchart to illustrate key steps in the interpretation of genetic variants to identify autosomal dominant (likely) pathogenic variants for clinical diagnostic or research reporting. gnomAD, Genome Aggregation Database. How should expert disease-related knowledge guide the interpretation and reporting of genetic variants that might cause autosomal dominant monogenic disease? Do not analyze genes without robust evidence to support the gene-disease association (6), for example the BLK, KLF11, and PAX4 genes, where current evidence is limited (7). Reputable clinical diagnostic laboratories do not include these genes in their monogenic diabetes testing. Do not report a heterozygous variant in autosomal recessive disorders caused by biallelic variants (homozygous or compound heterozygous). For example, biallelic pathogenic WFS1 variants cause Wolfram syndrome (8), a very rare disorder with an estimated prevalence of 1 in 500,000 (heterozygous carrier frequency ~0.3%). WFS1 is an extremely polymorphic gene with rare (allele frequency < 0.1%) missense variants present in more than 2% of the population. Although there are reports of autosomal dominant diabetes caused by heterozygous WFS1 variants, these are extremely rare: one family with dominantly inherited nonsyndromic diabetes (9) and five patients with neonatal- or infancy-onset diabetes, deafness, and cataracts (10). The finding of a rare heterozygous variant is therefore highly unlikely to be causative of monogenic diabetes and should not be reported. Use appropriate gene-specific allele frequency cutoffs in control population data to exclude variants that are too common to be highly penetrant disease-causing variants. For example, Ming-Qiang et al. found that PAX4 variants were the second most common cause of monogenic diabetes in their Chinese cohort (3), but the missense variants they reported are present in more than 1% of the East Asian population cohort (approximately 15,000 individuals) in the publicly available gnomAD database (https://gnomad.broadinstitute.org) (11). A tool is available (http://cardiodb.org/alleleFrequencyApp) that allows the user to input inheritance mode, disease prevalence, penetrance, genetic heterogeneity (how many cases can be attributed to the gene), and allelic heterogeneity (how many cases can be attributed to a single variant) and calculate a maximum credible allele frequency (12). Using HNF1A monogenic diabetes as an example with monoallelic inheritance, disease prevalence of 1 in 10,000, allelic heterogeneity 0.16, genetic heterogeneity 0.35, and penetrance 0.95, the maximum tolerated pathogenic allele count is 2 in the gnomAD database (n = 141,456). In a study of diabetic subjects from South India, Mohan et al. reported HNF1A variants as the most common subtype of monogenic diabetes in their study (1). However, six of the 11 patients had variants that are too common in the European ancestry population in gnomAD (allele counts of 4 or more in approximately 60,000 Europeans) to be highly penetrant variants causative of monogenic diabetes. It is essential to check the variant frequency in large variant data sets to avoid this type of misclassification. Check that the most clinically relevant transcript is used. For example, there are multiple isoforms of the transcription factor HNF4A. For interpretation of monogenic diabetes variants, the messenger RNA transcript that encodes the pancreatic isoform, rather than the liver isoform, should be used because there is a pancreatic specific promoter and exon 1 (NM_175914.4). Using this transcript, the HNF4A variant p.A417T Yu et al. reported (4) is noncoding (c.1063+120) and likely benign. Identify the specific subtypes of heterozygous mutations that result in the specific change of function required to cause monogenic disease. Heterozygous pathogenic variants in the GCK, HNF1A, HNF1B, and HNF4A genes cause diabetes by reducing the level of functional protein, described as haploinsufficiency (7). For other monogenic diabetes subtypes there is a different disease mechanism, and heterozygous predicted loss-of-function (frameshift, nonsense, or essential splice site) variants are not causative. The KCNJ11 and ABCC8 genes encode the subunits of the β cell potassium channel. Activating variants prevent the channel from closing in response to raised blood glucose, and this prevents insulin release in patients with diabetes (13). Recessive loss-of-function KCNJ11 and ABCC8 variants cause the opposite phenotype of hyperinsulinism (14). This means that a heterozygous loss of function variant in one of these genes confers carrier status for congenital hyperinsulinism but does not cause monogenic diabetes. Other examples include the CEL gene, where only variants within the first or fourth repeats of the VNTR region are pathogenic (15); RFX6, where there is only evidence to implicate protein truncating variants (16); and the sole heterozygous PDX1 pathogenic variant, p.P63fs, known to cause monogenic diabetes through a dominant negative effect (17). Exclude variants of uncertain significance. These are variants lacking evidence for classification as pathogenic or likely pathogenic (5). Examples include novel missense variants in constrained genes where the amino acid substitution is predicted to have a deleterious effect upon protein function. Any individual has about 100 variants of this type and should be treated as “uncertain until proven guilty” (18). Why are errors in the interpretation of genetic variants common in both academic and diagnostic reports? Misinterpretation of genetic variants is common, both in the published literature (19) and in reports from diagnostic laboratories. Next-generation sequencing technology has facilitated both the ease and scale of genetic testing, but obtaining genotype data is far more straightforward than interpreting it correctly. Academic studies often use bespoke criteria for defining pathogenicity rather than applying guidelines developed to improve the quality and consistency of variant interpretation (5). Studies may base their variant classifications solely on in silico prediction of pathogenicity using tools such as REVEL or SIFT, PolyPhen, and MutationTaster that provide only supporting evidence within the ACMG/AMP guidelines framework recommended for diagnostic reporting (5). The availability of large variant data sets such as the gnomAD (11) has shown that many previously reported pathogenic variants are too common to be highly penetrant disease-causing variants (20). In some cases the evidence supporting gene-disease associations is no longer valid, but publications refuting these genes are rare and may consider only a single putative mutation (21, 22). The utility of population variant databases will increase as more exome and genome sequence data are aggregated from a wider range of populations (11). An overemphasis on bioinformatic tools for predicting pathogenicity has resulted in false positive assertions. Although curated databases of pathogenic/likely pathogenic variants are widely used, the level of curating varies, and there are often insufficient data available for users to assess the provenance of individual variant pathogenicity assertions. The prior probability of a monogenic etiology is an important consideration for variant classification. For monogenic diabetes the prior probability will be low because only a small proportion of patients with diabetes have a monogenic subtype (3.6% of patients diagnosed at age ≤ 30 years; ref. 23). Sensitivity/specificity estimates for pathogenicity prediction tools like REVEL and PolyPhen are calculated from a set of pathogenic and benign variants in genes with a higher likelihood of a monogenic etiology (24). How can the accuracy of variant interpretation and reporting be improved? A number of initiatives are addressing various aspects of variant interpretation. For example the NIH-funded ClinGen resource (https://clinicalgenome.org/) includes curating of gene-disease validity evidence, the ClinVar variant repository, and expert groups developing gene- or disease-specific criteria for variant classification. Sharing genetic variant data on a global scale is an essential requirement (25). The ACMG/AMP variant classification guidelines have been adopted in many countries, and we recommend that all academic studies use these guidelines for variant classification (5). Genetic testing for clinical diagnosis should be performed in an accredited laboratory that participates in external quality assessment schemes that include variant classification. Conclusion We have entered a new era in which the generation of massive quantities of accurate genetic data from an individual is no longer difficult, but the new challenge is how to correctly interpret this data. This Viewpoint emphasizes how disease-specific expertise is required when interpreting genetic data and how failure to use this information will result in errors. Misdiagnosis not only affects the individual patients for whom testing is being performed but also can be amplified through predictive testing of relatives and use of incorrect variant classifications in databases and publications for interpretation of the same variant in other patients. Accurate genetic diagnosis is needed to predict disease prognosis and guide clinical management. Acknowledgments SE and ATH are Wellcome Senior Investigators (098395/Z/12/Z). ATH is a Senior Investigator at the National Institute for Health Research and is supported by the National Institute for Health Research Exeter Clinical Research Facility. KAP has a postdoctoral fellowship funded by the Wellcome Trust (110082/Z/15/Z). Footnotes Conflict of interest: The authors have declared that no conflict of interest exists. Copyright: © 2020, American Society for Clinical Investigation. Reference information: J Clin Invest. 2020;130(1):14–16. https://doi.org/10.1172/JCI133516. References Mohan V, et al. Comprehensive genomic analysis identifies pathogenic variants in maturity-onset diabetes of the young (MODY) patients in South India. BMC Med Genet. 2018;19(1):22. View this article via: PubMedCrossRefGoogle Scholar Pezzilli S, et al. Insights from molecular characterization of adult patients of families with multigenerational diabetes. 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There has been consistent interest in bolstering the physician-scientist workforce to fuel discovery and translational research (1, 2). In 2014, the Physician-Scientist Workforce Working Group assembled by the NIH identified increasing diversity of the physician-scientist workforce as a priority for the future advancement of the profession; at the time, almost three-quarters of NIH research project grant recipients with an MD-PhD were White, and greater than two-thirds were male (3, 4). Even so, women and underrepresented minorities (URMs), which include Black/African Americans, Hispanics/Latinos, and Native Americans/American Indians, remain underrepresented. The enrollment data for 2018–2019 show that women made up 39.9% of matriculated MD-PhD students, up from 37.7% in 2014–2015 (5). In the past five years, the rate for women enrolled has increased at about 0.55% per year. Even if growth continued at the 2018–2019 rate (1.1%), it would take another ten years for parity to be reached between men and women enrolled in MD-PhD programs. Similar trends emerge for URM MD-PhD students: the graduating class of 2018 had 13.8% URM graduates, whereas 2018–2019 matriculants included 12.1% URMs (6, 7). For that academic year, 16% of applicants were URMs (8). These data highlight that there has been almost no growth in the number of URM MD-PhD students matriculating compared with those who matriculated 8–10 years prior (i.e., graduating class of 2018). Additionally, it is necessary to examine reasons why potential women and URM applicants decide not to apply to MD-PhD programs from the outset. The story admissions statistics tell Potential applicants spend considerable time on the internet looking for information about individual MD-PhD programs. A study focused on minority students who applied to medical school revealed that “[t]he few [participants] who searched school websites for information about the admissions process reported that the quality of the websites mattered, being critical resources for students with no other access to information” (9). Although the study population focused on medical students, this suggests that providing accurate and clear data on websites could be a way of raising awareness about programs for women and URM applicants with no other source of reliable information about applying, such as a mentor, family member, or pre-health advisor. URM premedical students cite lack of mentorship and advising as a barrier to applying to medical school, with some receiving information when they felt it was too late, leaving them at a disadvantage (10). Data on premedical women college students show that they are more likely than male undergraduates to view premedical course grades as a barrier to medical school admission (11). Thus, potential applicants look online for details to inform whether or not they should apply in order to maximize their chances relative to the upfront costs of applying. Applicants have access to the Medical School Admissions Requirements database if they purchase it through the Association of American Medical Colleges (AAMC), which compiles statistics such as grade point average (GPA) and Medical College Admission Test (MCAT) scores that are useful for those creating a list of schools to which to apply. However, these data are not as useful for those applying to MD-PhD programs, who have a slightly different application process. For MD-PhD applicants, quantity and quality of research experience often play into the admissions decision, but this is difficult to compare across applicants, since many (29.7%) who end up matriculating in programs have at least one year of prior research (12). Therefore, potential applicants may try to use metrics that can be compared among applicants, such as MCAT score or GPA, to guide their application process. Some potential applicants might even turn to anonymous online forums such as Student Doctor Network and Reddit, where they can scroll through posts to gauge their chances of being considered for, and accepted into, an MD-PhD program. The self-selection bias of those who post on these sites may paint an unbalanced picture of who is applying, and the advice provided is given by anyone on the internet, whether or not they are familiar with the admissions procedures at different programs. Furthermore, postings represent the perception of just one person using a pseudonym, so their reliability cannot be confirmed. Some potential applicants may come across statistics published by the AAMC that show the mean, minimum, and maximum GPA and MCAT scores for MD-PhD matriculants. For 2018 matriculants the mean GPA was 3.79 ± 0.19 with a range of 2.68–4.00, and the mean MCAT score was 515.6 ± 5.6 with a range of 497–528 (13). These data can be both intimidating and comforting. The data are intimidating if one considers the means and standard deviations, which suggest a distribution with a very negative skew, with 50 percent of matriculants earning an MCAT score above the 92nd percentile or having a GPA greater than 3.8. However, the data might be comforting to some because the minimum GPA and MCAT composite score of matriculants are 2.75 and 495.0, respectively. It should also be noted that a study of MD-PhD enrollees who took the MCAT in the early 2000s showed that 92.1% of applicants had an MCAT score in the upper two quintiles, which may be daunting to those with lower scores (14). The fact that this information can be both intimidating and comforting simply adds to the uncertainty of potential applicants trying to determine whether they are competitive. The MCAT and GPA data on interviewees, accepted applicants, and matriculants provided by MD-PhD programs vary drastically. Searching the internet in late June 2019, we identified that 116 of 121 MD-PhD programs had a website with specific admissions-related details. More than 50 percent of programs included no information regarding MCAT score or GPA for individuals who applied to, interviewed at, were accepted to, or matriculated into their program (Figure 1). One-fifth of program websites listed a mean MCAT score and GPA; the majority did not include a standard deviation, making the mean difficult to interpret. Less than ten percent of programs included a range for these statistics on their website, although NIH-funded Medical Scientist Training Programs were more likely than other MD-PhD programs to include a range (13% vs. 1%, respectively). Figure 1 Categories of admissions statistics reported by MD-PhD programs on their websites. (A) MCAT exam scores. (B) Grade point averages. Pie charts represent the data for all MD-PhD programs (left), Medical Scientist Training Programs (MSTPs; middle), and other MD-PhD programs (right). The colors represent the categories of admissions statistics (minimum, median, mean, range, and no statistics reported) presented on the websites. These data points are used by potential applicants as critical information when deciding whether and where to apply. Therefore, these data can serve to encourage more potential applicants to submit applications because they may feel more qualified, or they can be a deterrent, depending on how they are presented. Similarly, information (e.g., means without standard deviations) suggesting that only those with high scores are accepted into a program may contribute to self-selection by women and URM applicants out of the application process due to fear of not being sufficiently qualified. The lack of accurate information may be feeding into imposter syndrome for women and URM applicants and thus acting as a deterrent. Interestingly, women are more likely to apply to lower-ranking MD-PhD programs, again suggesting that some applicants may be applying depending on the programs for which they believe they are qualified (15). Imposter syndrome Students battling impostor syndrome feel they are not smart or talented enough to pursue this profession (16). Furthermore, they live in constant fear that they will be exposed as a fraud and asked to leave their program. This perception is internalized and over time eats away at their self-confidence. The fear, when exacerbated, can result in anxiety, stress, or depression (17). Imposter syndrome is manifested by comparing oneself to others, not feeling academically prepared and on par with peers, and questioning the validity of one’s acceptance into a program (18, 19). The literature about the experience of premedical students, especially women and minorities, is currently limited. However, there is evidence for increased attrition of these groups in premedical required courses and STEM majors due to seeing grades and GPA as a marker of competency or fit for the career path (11, 20, 21). The fear associated with imposter syndrome may cause individuals not to apply if they do not feel they are the perfect applicant with average or above-average MCAT scores and GPA. Lack of knowledge as to the full ranges of these scores does little to alleviate their concerns. Redefining the ideal MD-PhD candidate Having clear and accessible information on successful applicants to individual programs would be a simple step toward improving equity in the MD-PhD application process. Publishing the range of MCAT scores and GPAs of those that a program has accepted, perhaps over a range of time such as ten years, would allow those considering applying to make informed decisions about their candidacy. In this way, women and URM applicants who may have been deterred by lack of information or misleading high-mean statistics for many programs would instead have sufficient information that might make them more likely to apply. Pooling the data for accepted students over a certain period of time would ensure that this range would not identify individuals who matriculate at smaller programs or specific individuals in a matriculating class. Above all, this strategy would be a simple step toward redefining the manufactured image of academic perfection (i.e., high GPA and MCAT score with many publications) that many believe represents those who will be successful applicants and future physician-scientists. Acknowledgments BC was supported by a Medical Scientist Training Program grant from the National Institute of General Medical Sciences of the NIH under award number T32GM007739 to the Weill Cornell/Rockefeller/Memorial Sloan Kettering Tri-Institutional MD-PhD Program. Footnotes Conflict of interest: The authors have declared that no conflict of interest exists. Copyright: © 2020, American Society for Clinical Investigation. Reference information: J Clin Invest. 2020;130(1):17–19. https://doi.org/10.1172/JCI134941. References Daye D, Patel CB, Ahn J, Nguyen FT. Challenges and opportunities for reinvigorating the physician-scientist pipeline. 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High-throughput technologies for genomics, transcriptomics, proteomics, and metabolomics, and integrative analysis of these data, enable new, systems-level insights into disease pathogenesis. Mitochondrial diseases are an excellent target for hypothesis-generating omics approaches, as the disease group is mechanistically exceptionally complex. Although the genetic background in mitochondrial diseases is in either the nuclear or the mitochondrial genome, the typical downstream effect is dysfunction of the mitochondrial respiratory chain. However, the clinical manifestations show unprecedented variability, including either systemic or tissue-specific effects across multiple organ systems, with mild to severe symptoms, and occurring at any age. So far, the omics approaches have provided mechanistic understanding of tissue-specificity and potential treatment options for mitochondrial diseases, such as metabolome remodeling. However, no curative treatments exist, suggesting that novel approaches are needed. In this Review, we discuss omics approaches and discoveries with the potential to elucidate mechanisms of and therapies for mitochondrial diseases.

Advanced phenotyping of cardiovascular diseases has evolved with the application of high-resolution omics screening to populations enrolled in large-scale observational and clinical trials. This strategy has revealed that considerable heterogeneity exists at the genotype, endophenotype, and clinical phenotype levels in cardiovascular diseases, a feature of the most common diseases that has not been elucidated by conventional reductionism. In this discussion, we address genomic context and (endo)phenotypic heterogeneity, and examine commonly encountered cardiovascular diseases to illustrate the genotypic underpinnings of (endo)phenotypic diversity. We highlight the existing challenges in cardiovascular disease genotyping and phenotyping that can be addressed by the integration of big data and interpreted using novel analytical methodologies (network analysis). Precision cardiovascular medicine will only be broadly applied to cardiovascular patients once this comprehensive data set is subjected to unique, integrative analytical strategies that accommodate molecular and clinical heterogeneity rather than ignore or reduce it.

The discovery of peripheral intracellular clocks revealed circadian oscillations of clock genes and their targets in all cell types, including those in the lung, sparking exploration of clocks in lung disease pathophysiology. While the focus has been on the role of these clocks in adult airway diseases, clock biology is also likely to be important in perinatal lung development, where it has received far less attention. Historically, fetal circadian rhythms have been considered irrelevant owing to lack of external light exposure, but more recent insights into peripheral clock biology raise questions of clock emergence, its concordance with tissue-specific structure/function, the interdependence of clock synchrony and functionality in perinatal lung development, and the possibility of lung clocks in priming the fetus for postnatal life. Understanding the perinatal molecular clock may unravel mechanistic targets for chronic airway disease across the lifespan. With current research providing more questions than answers, it is about time to investigate clocks in the developing lung.

Immunotherapy has transformed the treatment landscape for a wide range of human cancers. Immune checkpoint inhibitors (ICIs), monoclonal antibodies that block the immune-regulatory “checkpoint” receptors CTLA-4, PD-1, or its ligand PD-L1, can produce durable responses in some patients. However, coupled with their success, these treatments commonly evoke a wide range of immune-related adverse events (irAEs) that can affect any organ system and can be treatment-limiting and life-threatening, such as diabetic ketoacidosis, which appears to be more frequent than initially described. The majority of irAEs from checkpoint blockade involve either barrier tissues (e.g., gastrointestinal mucosa or skin) or endocrine organs, although any organ system can be affected. Often, irAEs resemble spontaneous autoimmune diseases, such as inflammatory bowel disease, autoimmune thyroid disease, type 1 diabetes mellitus (T1D), and autoimmune pancreatitis. Yet whether similar molecular or pathologic mechanisms underlie these apparent autoimmune adverse events and classical autoimmune diseases is presently unknown. Interestingly, evidence links HLA alleles associated with high risk for autoimmune disease with ICI-induced T1D and colitis. Understanding the genetic risks and immunologic mechanisms driving ICI-mediated inflammatory toxicities may not only identify therapeutic targets useful for managing irAEs, but may also provide new insights into the pathoetiology and treatment of autoimmune diseases.

Mitochondrial dysfunction or loss is evident in neurodegenerative diseases. Furthermore, mitochondrial DNA (mtDNA) mutations associated with NADH dehydrogenase subunits and nuclear gene mutations that affect mitochondrial function result in optic neuropathies. In this issue of the JCI, Del Dotto et al. and Piro-Mégy et al. identify heterozygous mutations in nuclear-encoded mitochondrial single-strand binding protein 1 (SSBP1) in patients with apparently dominant optic neuropathy with or without extraocular phenotypes. Both research groups reported similar mitochondrial findings in response to SSBP1 mutations. However, the specific SSBP1 mitochondria–associated function in retinal ganglion cells (RGCs) and the resulting optic nerve remains unclear. We suggest that high expression of SSBP1 during RGC differentiation is critical for mtDNA maintenance to produce appropriate optic nerve connectivity and that SSBP1 mutations in dominant optic atrophy patients do not permit stable binding to N6-methyldeoxyadenosine on the heavy strand involved with replication, leading to disruptions of mtDNA and, eventually, optic nerve dysfunction.

Brown adipose tissue (BAT) contains mitochondria-enriched thermogenic fat cells (brown adipocytes) that play a crucial role in the regulation of energy metabolism and systemic glucose homeostasis. It was presumed that brown adipocytes are composed of a homogeneous cell population. In this issue of the JCI, however, Song and colleagues report a previously uncharacterized subpopulation of brown adipocytes that display distinct characteristics from the conventional brown adipocytes in their molecular signature, regulation, and fuel utilization. The present study provides novel insight into our understanding of cellular heterogeneity in adipose tissues.

Unconventional T cell subsets, including donor-unrestricted T cells (DURTs) and γδ T cells, are promising new players in the treatment and prevention of infectious diseases. In this issue of the JCI, Ogongo et al. used T cell receptor (TCR) sequencing to characterize unconventional T cell subsets in surgical lung resections and blood from Mycobacterium tuberculosis–infected (Mtb-infected) individuals with and without HIV coinfection. The study revealed highly localized expansions of γδ T cell clonotypes not previously associated with the immune response to Mtb and demonstrates the power of high-throughput analysis of the TCR repertoire directly from infected tissue. The findings contribute to our understanding of tuberculosis control and have implications for the development of both therapeutic and vaccination strategies.

Pancreatic ductal adenocarcinomas (PDACs) are classically immunologically cold tumors that have failed to demonstrate a significant response to immunotherapeutic strategies. This feature is attributed to both the immunosuppressive tumor microenvironment (TME) and limited immune cell access due to the surrounding stromal barrier, a histological hallmark of PDACs. In this issue of the JCI, Sharma et al. employ a broad glutamine antagonist, 6-diazo-5-oxo-l-norleucine (DON), to target a metabolic program that underlies both PDAC growth and hyaluronan production. Their findings describe an approach to converting the PDAC TME into a hot TME, thereby empowering immunotherapeutic strategies such as anti-PD1 therapy.

Albuminuria acts as a marker of progressive chronic kidney disease and as an indicator for initiation of hypertension treatment via modulation of the renin-angiotensin-aldosterone system with angiotensin receptor blockers or angiotensin-converting enzyme inhibitors. However, the true significance of albuminuria has yet to be fully defined. Is it merely a marker of underlying pathophysiology, or does it play a causal role in the progression of kidney disease? The answer remains under debate. In this issue of the JCI, Bedin et al. used next-generation sequencing data to identify patients with chronic proteinuria who had biallelic variants in the cubilin gene (CUBN). Through investigation of these pathogenic mutations in CUBN, the authors have further illuminated the clinical implications of albuminuria.

Excessive fecal bile acid (BA) loss causes symptoms in a large proportion of people diagnosed with irritable bowel syndrome with diarrhea, a common functional bowel disorder. This BA diarrhea (BAD) results from increased hepatic synthesis of BAs, with impaired negative feedback regulation by the ileal hormone fibroblast growth factor 19 (FGF19). In this issue of the JCI, Zhao et al. investigated BA metabolism, including fecal BAs, serum BAs, and FGF19, in patients and controls. They identified associations between fecal bacterial BA metabolism and specific microbiota, especially Clostridium scindens. These findings have been tested in a mouse model using microbiota transplants and antibiotic treatment. This group of organisms has potential as a biomarker for BAD and to be a target for therapy.

XMEN (X-linked immunodeficiency with magnesium defect, EBV infection, and neoplasia) is a complex primary immunological deficiency caused by mutations in MAGT1, a putative magnesium transporter. In this issue of the JCI, Ravell et al. greatly expand the clinical picture. The authors investigated patients’ mutations and symptoms and reported distinguishing immunophenotypes. They also showed that MAGT1 is required for N-glycosylation of key T cell and NK cell receptors that can account for some of the clinical features. Notably, transfection of the affected lymphocytes with MAGT1 mRNA restored both N-glycosylation and receptor function. Now we can add XMEN to the ever-growing family of congenital disorders of glycosylation (CDG).

The mineralocorticoid aldosterone is produced in the adrenal zona glomerulosa (ZG) under the control of the renin–angiotensin II (AngII) system. Primary aldosteronism (PA) results from renin-independent production of aldosterone and is a common cause of hypertension. PA is caused by dysregulated localization of the enzyme aldosterone synthase (Cyp11b2), which is normally restricted to the ZG. Cyp11b2 transcription and aldosterone production are predominantly regulated by AngII activation of the Gq signaling pathway. Here, we report the generation of transgenic mice with Gq-coupled designer receptors exclusively activated by designer drugs (DREADDs) specifically in the adrenal cortex. We show that adrenal-wide ligand activation of Gq DREADD receptors triggered disorganization of adrenal functional zonation, with induction of Cyp11b2 in glucocorticoid-producing zona fasciculata cells. This result was consistent with increased renin-independent aldosterone production and hypertension. All parameters were reversible following termination of DREADD-mediated Gq signaling. These findings demonstrate that Gq signaling is sufficient for adrenocortical aldosterone production and implicate this pathway in the determination of zone-specific steroid production within the adrenal cortex. This transgenic mouse also provides an inducible and reversible model of hyperaldosteronism to investigate PA therapeutics and the mechanisms leading to the damaging effects of aldosterone on the cardiovascular system.

Sustained, indolent immune injury of the vasculature of a heart transplant limits long-term graft and recipient survival. This injury is mitigated by a poorly characterized, maladaptive repair response. Vascular endothelial cells respond to proangiogenic cues in the embryo by differentiation to specialized phenotypes, associated with expression of apelin. In the adult, the role of developmental proangiogenic cues in repair of the established vasculature is largely unknown. We found that human and minor histocompatibility–mismatched donor mouse heart allografts with alloimmune-mediated vasculopathy upregulated expression of apelin in arteries and myocardial microvessels. In vivo, loss of donor heart expression of apelin facilitated graft immune cell infiltration, blunted vascular repair, and worsened occlusive vasculopathy in mice. In vitro, an apelin receptor agonist analog elicited endothelial nitric oxide synthase activation to promote endothelial monolayer wound repair and reduce immune cell adhesion. Thus, apelin acted as an autocrine growth cue to sustain vascular repair and mitigate the effects of immune injury. Treatment with an apelin receptor agonist after vasculopathy was established markedly reduced progression of arterial occlusion in mice. Together, these initial data identify proangiogenic apelin as a key mediator of coronary vascular repair and a pharmacotherapeutic target for immune-mediated injury of the coronary vasculature.

Inherited optic neuropathies include complex phenotypes, mostly driven by mitochondrial dysfunction. We report an optic atrophy spectrum disorder, including retinal macular dystrophy and kidney insufficiency leading to transplantation, associated with mitochondrial DNA (mtDNA) depletion without accumulation of multiple deletions. By whole-exome sequencing, we identified mutations affecting the mitochondrial single-strand binding protein (SSBP1) in 4 families with dominant and 1 with recessive inheritance. We show that SSBP1 mutations in patient-derived fibroblasts variably affect the amount of SSBP1 protein and alter multimer formation, but not the binding to ssDNA. SSBP1 mutations impaired mtDNA, nucleoids, and 7S-DNA amounts as well as mtDNA replication, affecting replisome machinery. The variable mtDNA depletion in cells was reflected in severity of mitochondrial dysfunction, including respiratory efficiency, OXPHOS subunits, and complex amount and assembly. mtDNA depletion and cytochrome c oxidase–negative cells were found ex vivo in biopsies of affected tissues, such as kidney and skeletal muscle. Reduced efficiency of mtDNA replication was also reproduced in vitro, confirming the pathogenic mechanism. Furthermore, ssbp1 suppression in zebrafish induced signs of nephropathy and reduced optic nerve size, the latter phenotype complemented by WT mRNA but not by SSBP1 mutant transcripts. This previously unrecognized disease of mtDNA maintenance implicates SSBP1 mutations as a cause of human pathology.

Arcuate nucleus agouti–related peptide (AgRP) neurons play a central role in feeding and are under complex regulation by both homeostatic hormonal and nutrient signals and hypothalamic neuronal pathways. Feeding may also be influenced by environmental cues, sensory inputs, and other behaviors, implying the involvement of higher brain regions. However, whether such pathways modulate feeding through direct synaptic control of AgRP neuron activity is unknown. Here, we show that nociceptin-expressing neurons in the anterior bed nuclei of the stria terminalis (aBNST) make direct GABAergic inputs onto AgRP neurons. We found that activation of these neurons inhibited AgRP neurons and feeding. The activity of these neurons increased upon food availability, and their ablation resulted in obesity. Furthermore, these neurons received afferent inputs from a range of upstream brain regions as well as hypothalamic nuclei. Therefore, aBNST GABAergic nociceptin neurons may act as a gateway to feeding behavior by connecting AgRP neurons to both homeostatic and nonhomeostatic neuronal inputs.

Mutations in genes encoding components of the mitochondrial DNA (mtDNA) replication machinery cause mtDNA depletion syndromes (MDSs), which associate ocular features with severe neurological syndromes. Here, we identified heterozygous missense mutations in single-strand binding protein 1 (SSBP1) in 5 unrelated families, leading to the R38Q and R107Q amino acid changes in the mitochondrial single-stranded DNA-binding protein, a crucial protein involved in mtDNA replication. All affected individuals presented optic atrophy, associated with foveopathy in half of the cases. To uncover the structural features underlying SSBP1 mutations, we determined a revised SSBP1 crystal structure. Structural analysis suggested that both mutations affect dimer interactions and presumably distort the DNA-binding region. Using patient fibroblasts, we validated that the R38Q variant destabilizes SSBP1 dimer/tetramer formation, affects mtDNA replication, and induces mtDNA depletion. Our study showing that mutations in SSBP1 cause a form of dominant optic atrophy frequently accompanied with foveopathy brings insights into mtDNA maintenance disorders.

Whether respiratory epithelial cells regulate the final transit of extravasated neutrophils into the inflamed airspace or are a passive barrier is poorly understood. Alveolar epithelial type 1 (AT1) cells, best known for solute transport and gas exchange, have few established immune roles. Epithelial membrane protein 2 (EMP2), a tetraspan protein that promotes recruitment of integrins to lipid rafts, is highly expressed in AT1 cells but has no known function in lung biology. Here, we show that Emp2–/– mice exhibit reduced neutrophil influx into the airspace after a wide range of inhaled exposures. During bacterial pneumonia, Emp2–/– mice had attenuated neutrophilic lung injury and improved survival. Bone marrow chimeras, intravital neutrophil labeling, and in vitro assays suggested that defective transepithelial migration of neutrophils into the alveolar lumen occurs in Emp2–/– lungs. Emp2–/– AT1 cells had dysregulated surface display of multiple adhesion molecules, associated with reduced raft abundance. Epithelial raft abundance was dependent upon putative cholesterol-binding motifs in EMP2, whereas EMP2 supported adhesion molecule display and neutrophil transmigration through suppression of caveolins. Taken together, we propose that EMP2-dependent membrane organization ensures proper display on AT1 cells of a suite of proteins required to instruct paracellular neutrophil traffic into the alveolus.

Mosaic-variegated aneuploidy (MVA) syndrome is a rare childhood disorder characterized by biallelic BUBR1, CEP57, or TRIP13 aberrations; increased chromosome missegregation; and a broad spectrum of clinical features, including various cancers, congenital defects, and progeroid pathologies. To investigate the mechanisms underlying this disorder and its phenotypic heterogeneity, we mimicked the BUBR1L1012P mutation in mice (BubR1L1002P) and combined it with 2 other MVA variants, BUBR1X753 and BUBR1H, generating a truncated protein and low amounts of wild-type protein, respectively. Whereas BubR1X753/L1002P and BubR1H/X753 mice died prematurely, BubR1H/L1002P mice were viable and exhibited many MVA features, including cancer predisposition and various progeroid phenotypes, such as short lifespan, dwarfism, lipodystrophy, sarcopenia, and low cardiac stress tolerance. Strikingly, although these mice had a reduction in total BUBR1 and spectrum of MVA phenotypes similar to that of BubR1H/H mice, several progeroid pathologies were attenuated in severity, which in skeletal muscle coincided with reduced senescence-associated secretory phenotype complexity. Additionally, mice carrying monoallelic BubR1 mutations were prone to select MVA-related pathologies later in life, with predisposition to sarcopenia correlating with mTORC1 hyperactivity. Together, these data demonstrate that BUBR1 allelic effects beyond protein level and aneuploidy contribute to disease heterogeneity in both MVA patients and heterozygous carriers of MVA mutations.

Currently, an effective targeted therapy for pancreatitis is lacking. Hereditary pancreatitis (HP) is a heritable, autosomal-dominant disorder with recurrent acute pancreatitis (AP) progressing to chronic pancreatitis (CP) and a markedly increased risk of pancreatic cancer. In 1996, mutations in PRSS1 were linked to the development of HP. Here, we developed a mouse model by inserting a full-length human PRSS1R122H gene, the most commonly mutated gene in human HP, into mice. Expression of PRSS1R122H protein in the pancreas markedly increased stress signaling pathways and exacerbated AP. After the attack of AP, all PRSS1R122H mice had disease progression to CP, with similar histologic features as those observed in human HP. By comparing PRSS1R122H mice with PRSS1WT mice, as well as enzymatically inactivated Dead-PRSS1R122H mice, we unraveled that increased trypsin activity is the mechanism for R122H mutation to sensitize mice to the development of pancreatitis. We further discovered that trypsin inhibition, in combination with anticoagulation therapy, synergistically prevented progression to CP in PRSS1R122H mice. These animal models help us better understand the complex nature of this disease and provide powerful tools for developing and testing novel therapeutics for human pancreatitis.

Multiple sclerosis (MS) is an inflammatory, demyelinating disease of the CNS. Although CD4+ T cells are implicated in MS pathogenesis and have been the main focus of MS research using the animal model experimental autoimmune encephalomyelitis (EAE), substantial evidence from patients with MS points to a role for CD8+ T cells in disease pathogenesis. We previously showed that an MHC class I–restricted epitope of myelin basic protein (MBP) is presented in the CNS during CD4+ T cell–initiated EAE. Here, we investigated whether naive MBP-specific CD8+ T cells recruited to the CNS during CD4+ T cell–initiated EAE engaged in determinant spreading and influenced disease. We found that the MBP-specific CD8+ T cells exacerbated brain but not spinal cord inflammation. We show that a higher frequency of monocytes and monocyte-derived cells presented the MHC class I–restricted MBP ligand in the brain compared with the spinal cord. Infiltration of MBP-specific CD8+ T cells enhanced ROS production in the brain only in these cell types and only when the MBP-specific CD8+ T cells expressed Fas ligand (FasL). These results suggest that myelin-specific CD8+ T cells may contribute to disease pathogenesis via a FasL-dependent mechanism that preferentially promotes lesion formation in the brain.

Unconventional T cells that recognize mycobacterial antigens are of great interest as potential vaccine targets against tuberculosis (TB). This includes donor-unrestricted T cells (DURTs), such as mucosa-associated invariant T cells (MAITs), CD1-restricted T cells, and γδ T cells. We exploited the distinctive nature of DURTs and γδ T cell receptors (TCRs) to investigate the involvement of these T cells during TB in the human lung by global TCR sequencing. Making use of surgical lung resections, we investigated the distribution, frequency, and characteristics of TCRs in lung tissue and matched blood from individuals infected with TB. Despite depletion of MAITs and certain CD1-restricted T cells from the blood, we found that the DURT repertoire was well preserved in the lungs, irrespective of disease status or HIV coinfection. The TCRδ repertoire, in contrast, was highly skewed in the lungs, where it was dominated by Vδ1 and distinguished by highly localized clonal expansions, consistent with the nonrecirculating lung-resident γδ T cell population. These data show that repertoire sequencing is a powerful tool for tracking T cell subsets during disease.

The c-MYC (MYC) oncoprotein is often overexpressed in human breast cancer; however, its role in driving disease phenotypes is poorly understood. Here, we investigate the role of MYC in HER2+ disease, examining the relationship between HER2 expression and MYC phosphorylation in HER2+ patient tumors and characterizing the functional effects of deregulating MYC expression in the murine NeuNT model of amplified-HER2 breast cancer. Deregulated MYC alone was not tumorigenic, but coexpression with NeuNT resulted in increased MYC Ser62 phosphorylation and accelerated tumorigenesis. The resulting tumors were metastatic and associated with decreased survival compared with NeuNT alone. MYC;NeuNT tumors had increased intertumoral heterogeneity including a subtype of tumors not observed in NeuNT tumors, which showed distinct metaplastic histology and worse survival. The distinct subtypes of MYC;NeuNT tumors match existing subtypes of amplified-HER2, estrogen receptor–negative human tumors by molecular expression, identifying the preclinical utility of this murine model to interrogate subtype-specific differences in amplified-HER2 breast cancer. We show that these subtypes have differential sensitivity to clinical HER2/EGFR–targeted therapeutics, but small-molecule activators of PP2A, the phosphatase that regulates MYC Ser62 phosphorylation, circumvents these subtype-specific differences and ubiquitously suppresses tumor growth, demonstrating the therapeutic utility of this approach in targeting deregulated MYC breast cancers.

Brown adipose tissue (BAT), as the main site of adaptive thermogenesis, exerts beneficial metabolic effects on obesity and insulin resistance. BAT has been previously assumed to contain a homogeneous population of brown adipocytes. Utilizing multiple mouse models capable of genetically labeling different cellular populations, as well as single-cell RNA sequencing and 3D tissue profiling, we discovered a brown adipocyte subpopulation with low thermogenic activity coexisting with the classical high-thermogenic brown adipocytes within the BAT. Compared with the high-thermogenic brown adipocytes, these low-thermogenic brown adipocytes had substantially lower Ucp1 and Adipoq expression, larger lipid droplets, and lower mitochondrial content. Functional analyses showed that, unlike the high-thermogenic brown adipocytes, the low-thermogenic brown adipocytes have markedly lower basal mitochondrial respiration, and they are specialized in fatty acid uptake. Upon changes in environmental temperature, the 2 brown adipocyte subpopulations underwent dynamic interconversions. Cold exposure converted low-thermogenic brown adipocytes into high-thermogenic cells. A thermoneutral environment had the opposite effect. The recruitment of high-thermogenic brown adipocytes by cold stimulation is not affected by high-fat diet feeding, but it does substantially decline with age. Our results revealed a high degree of functional heterogeneity of brown adipocytes.

Potentiating radiotherapy and chemotherapy by inhibiting DNA damage repair is proposed as a therapeutic strategy to improve outcomes for patients with solid tumors. However, this approach risks enhancing normal tissue toxicity as much as tumor toxicity, thereby limiting its translational impact. Using NU5455, a newly identified highly selective oral inhibitor of DNA-dependent protein kinase catalytic subunit (DNA-PKcs) activity, we found that it was indeed possible to preferentially augment the effect of targeted radiotherapy on human orthotopic lung tumors without influencing acute DNA damage or a late radiation-induced toxicity (fibrosis) to normal mouse lung. Furthermore, while NU5455 administration increased both the efficacy and the toxicity of a parenterally administered topoisomerase inhibitor, it enhanced the activity of doxorubicin released locally in liver tumor xenografts without inducing any adverse effect. This strategy is particularly relevant to hepatocellular cancer, which is treated clinically with localized drug-eluting beads and for which DNA-PKcs activity is reported to confer resistance to treatment. We conclude that transient pharmacological inhibition of DNA-PKcs activity is effective and tolerable when combined with localized DNA-damaging therapies and thus has promising clinical potential.

Diabetes is a common complication of cystic fibrosis (CF) that affects approximately 20% of adolescents and 40%–50% of adults with CF. The age at onset of CF-related diabetes (CFRD) (marked by clinical diagnosis and treatment initiation) is an important measure of the disease process. DNA variants associated with age at onset of CFRD reside in and near SLC26A9. Deep sequencing of the SLC26A9 gene in 762 individuals with CF revealed that 2 common DNA haplotypes formed by the risk variants account for the association with diabetes. Single-cell RNA sequencing (scRNA-Seq) indicated that SLC26A9 is predominantly expressed in pancreatic ductal cells and frequently coexpressed with CF transmembrane conductance regulator (CFTR) along with transcription factors that have binding sites 5′ of SLC26A9. These findings were replicated upon reanalysis of scRNA-Seq data from 4 independent studies. DNA fragments derived from the 5′ region of SLC26A9-bearing variants from the low-risk haplotype generated 12%–20% higher levels of expression in PANC-1 and CFPAC-1 cells compared with the high- risk haplotype. Taken together, our findings indicate that an increase in SLC26A9 expression in ductal cells of the pancreas delays the age at onset of diabetes, suggesting a CFTR-agnostic treatment for a major complication of CF.